The Women on Waves ship, which already has visited traditionally Roman Catholic countries Spain, Portugal and Ireland at the invitation of local women's groups, had planned to arrive at Smir, northern Morocco, but was denied entry.
"The harbor is totally blocked by warships so no one can get in, and there are a lot of police here," said Marlies Schellekens, a doctor from Women on Waves who had gone on shore.
"We're now working on an emergency plan but we have opened up our hotline so women can call for information about the abortion pill."
The group, which was invited to Morocco by rights group Alternative Movement for Individual Freedoms (MALI), wants to spread awareness on land about the use of pills for a medical abortion and said it would carry out abortions aboard the ship in international waters.
Like in other Muslim countries, abortion is illegal and punishable by up to 20 years in prison under Moroccan law, but hundreds of illegal abortions are carried out daily in clinics or using herbal medicines, sometimes resulting in death or injury.
"In Morocco, between 600 and 800 abortions are done every day, but only about 250 are done by doctors, so they are safer, while the rest are taking risks," Schellekens said.
There was no immediate comment from officials on Thursday, but on Wednesday Interior Minister Mohand Laenser, a secular member of the government led since December by moderate Islamists, said the ship would not be allowed to reach Morocco.
"The organizers have never contacted us to seek permission to visit Morocco," Laenser told Reuters. "Plus, we are not going to let them in."
Each year hundreds of single mothers are forced to abandon or give up their babies for adoption because of the stigma linked to abortion and pre-marital pregnancy.
The Moroccan Association Against Clandestine Abortion said in June that the legislation on abortion was disconnected from the social realities of the country and the number of unsafe abortion required a political commitment for a change.
Organisers of an all-gay cruise in June blamed Moroccan officials for the cancellation of what would have been the first visit of its kind to a Muslim country.